In terms of keeping the library itself encrypted, but still have the ability to auto-include (if that's what you're going for), I have no idea how to do that. But, there's a few options for keeping encrypted library files.

1) Use Deo's library. You can encrypt the file beforehand, decrypt them in the main script to use. You can even use #include; use #include *i, check if it was included (check a variable or something), then if it's not, decrypt it and reload the script. This will likely cause an error if you're calling functions though (function not found error). In that case, as mentioned, use a launcher script.

2) Use my PIN class. It's essentially an easy-to-use encrypted file wrapper for Deo's library. You can use the same methods I mentioned above.

In pretty much any case that full #include functionality is needed, you'll need a separate launcher.